Towards better reproducible practice

ANU BDSI
workshop
Reproducible research with Quarto

Emi Tanaka

Biological Data Science Institute

12th April 2024

Current learning objective

  • -Generate HTML, PDF, or Word documents using Markdown syntax
  • -Understand the anatomy of Quarto documents
  • -Develop dynamic documents containing code (in R, Python, or Julia) using Quarto
  • -Implement various code chunk options to customize chunk behaviour
  • Recognize the significance of reproducibility and grasp the concept of literate programming
  • Apply reproducible practices
  • Establish an organized folder structure for data projects

Non-Robust Workflow

What should have been submitted:

A Robust Workflow

  • Using a robust, reproducible workflow means:
    • you avoid manual, repetitive tasks
    • your results are computationally reproducible
  • Using a robust, reproducible workflow doesn’t mean you won’t make mistakes.
  • Practice of reproducibility just helps to minimise mistakes.

Literate Programming

Sharing your documents via RPubs

Happy sharing!

Summary